/etc/cron.d (and its brothers cron.daily/weekly/monthly) is preferred for all system crontabs. You shouldn't need to touch /etc/crontab.

It's essential to separate cron entries in multiple files, based on their functionality if you are planing to manage or automate things. Files under /etc/cron.d can be easily managed by packages or configuration management tools like puppet and chef. Root's crontab OTOH is practically un-maintenable by anything other than humans.

So in short, for system stuff you can use /etc/cron.*. If there's something you would like the root user to do then use root's crontab. /etc/crontab should be left untouched and managed by a package.